package shared

import scala.collection.immutable.SeqMap
import shared.Implicits._

/**
 * Created by yz on 21/7/2020
 */
object VarTool {

  val adminStr = "mole_pathology_admin"
  val userStr = "mole_pathology_user"
  val idStr = "mole_pathology_id"

  val dataHeaders = List("Tumor_Sample_Barcode", "Tumor_Sample_Name", "OncoTree_Code", "Chr", "Start", "End", "Ref", "Alt", "Func.refGene", "Gene.refGene", "GeneDetail.refGene", "ExonicFunc.refGene", "aaChangeRefGene", "cytoBand", "genomicSuperDups", "snp138", "Mutation.ratio", "1000g2015aug_all", "cosmic83", "CLNDSDBID", "CLNDBN", "CLNACC", "CLNDSDB", "CLINSIG", "SIFT_score", "SIFT_pred", "Polyphen2_HDIV_score", "Polyphen2_HDIV_pred", "Polyphen2_HVAR_score", "Polyphen2_HVAR_pred", "LRT_score", "LRT_pred", "MutationTaster_score", "MutationTaster_pred", "MutationAssessor_score", "MutationAssessor_pred", "FATHMM_score", "FATHMM_pred", "RadialSVM_score", "RadialSVM_pred", "LR_score", "LR_pred", "ExAC_ALL", "ExAC_AFR", "ExAC_AMR", "ExAC_EAS", "ExAC_FIN", "ExAC_NFE", "ExAC_OTH", "ExAC_SAS")
  val headerMap = SeqMap("barcode" -> "Tumor_Sample_Barcode", "sampleName" -> "Tumor_Sample_Name",
    "treeCode" -> "OncoTree_Code", "refGene" -> "Gene.refGene")
  val totalFieldNames = headerMap.keyList ::: dataHeaders.filterNot { x =>
    VarTool.headerMap.valueList.contains(x)
  }


}
